Changes between Version 123 and Version 124 of BigCompute

Timestamp:

Jul 3, 2011 1:45:40 PM (13 years ago)

Author:

Barbera van Schaik

Comment:

--

BigCompute

@@ -1 +1 @@
 [[TOC]]
 
-== Port applications to Dutch Life Science Grid ==
+== Analysis on the Dutch Life Science Grid ==
 '''People'''
-* AMC: Antoine van Kampen, Barbera van Schaik, Silvia D Olabarriaga, Mark Santcroos
+* UMCG: Freerk van Dijk, Morris Swertz
+* AMC: Barbera van Schaik, Mark Santcroos, Silvia D Olabarriaga, Antoine van Kampen
+* LUMC/TU Delft: Jan Bot, Kai Ye
 * Sara/BiGGrid: Tom Visser
-* UMCG: Morris Swertz, Freerk van Dijk
 
-=== Description ===
-Software is being implemented as workflow components. The workflows will run on the Dutch life science grid.
+== Data location ==
 
-* [http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/ Information about the infrastructure]
-* [http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/GettingStarted Getting started]
-* Angela CM Luyf, Barbera DC van Schaik, Michel de Vries, Frank Baas, Antoine HC van Kampen, Silvia D Olabarriaga (2010) '''Initial steps towards a production platform for DNA sequence analysis on the grid.''' BMC Bioinformatics 11: 1. Dec [http://www.ncbi.nlm.nih.gov/pubmed/21156038 pubmed] 
+Data is stored within the bbmri.nl virtual organisation (VO).
 
-=== Data access rights ===
+* [http://www.bbmriwiki.nl/wiki/BGIDatasets Location of GoNL data]
+* [http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/DataManagement More information about data management]
 
-To ensure that the most limited group of people has access to the data we have created a subgroup "gvnl" within the "vlemed" Virtual Organisation (VO).
-For people to become part of this group, it is required that they have a Grid certificate and that they are part of the "vlemed" VO.
-On the following page there is information on how to get a certificate, how to get into the "vlemed" VO: http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/EBioInfra#Access
-
-[http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/DataManagement More information about data access]
-
-== Data location on grid ==
-
-=== Data ===
-
-The data is located on the grid storage and only readable and writable for the vlemed/gvnl group.
-
-Storage location (LFC resource): lfc.grid.sara.nl
-
-Path: /grid/vlemed/gvnl/data
-
-URI: lfn://lfc.grid.sara.nl:5010/grid/vlemed/gvnl
-
-=== Workflows and databases ===
+== Workflow location ==
 
 * [BigComputeTemplates List of implemented workflows]
@@ -55 +36 @@
 The shell files can (in most cases) run on any linux cluster. In that case you need to place the shell file and the dependent executable(s) in one directory. At the start of each shell file is an example on how to run them.
 
-== Alternatives ==
-
-=== Clusters ===
+== Available systems ==
 
 * Groningen (Freerk)
@@ -68 +47 @@
 * DAS
 
-=== Grid ===
+== eScience related links ==
 
+* [https://grid.sara.nl/wiki/index.php/Main_Page Sara]
 * [http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/ EBioInfra]
+* [https://grid.sara.nl/wiki/index.php/Using_the_Grid/ToPoS Topos]
 * [http://www.cloud.sara.nl/ BiGGrid Cloud]
-* [https://grid.sara.nl/wiki/index.php/Using_the_Grid/ToPoS Topos]
+
+== Reading material e-!BioInfra ==
+
+* [http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/ Information about the infrastructure]
+* [http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/GettingStarted Getting started with workflows]
+* Angela CM Luyf, Barbera DC van Schaik, Michel de Vries, Frank Baas, Antoine HC van Kampen, Silvia D Olabarriaga (2010) '''Initial steps towards a production platform for DNA sequence analysis on the grid.''' BMC Bioinformatics 11: 1. Dec [http://www.ncbi.nlm.nih.gov/pubmed/21156038 pubmed] 
+
+== Reading material !ToPiCas ==
+
+* ADD REFERENCES HERE